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Pipeline remodelling. Issues 24, 31 and 36 #44

Merged
merged 173 commits into from
Mar 28, 2022
Merged

Pipeline remodelling. Issues 24, 31 and 36 #44

merged 173 commits into from
Mar 28, 2022

Commits on Nov 18, 2021

  1. Split out the config profiles (#43) 

    * Split out the config profiles

* Resolve the conflict using the upstream config
    @abhi18av
    abhi18av authored Nov 18, 2021
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Commits on Nov 19, 2021

  1. trying to have a create dbs process

    @fmalmeida
    fmalmeida committed Nov 19, 2021
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  2. found way to download dbs

    @fmalmeida
    fmalmeida committed Nov 19, 2021
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  3. adding resfinder and plasmidfinder download rules

    @fmalmeida
    fmalmeida committed Nov 19, 2021
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  4. added phigaro, vfdb and amrfinder download rules

    @fmalmeida
    fmalmeida committed Nov 19, 2021
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  5. added last database download rules

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  6. added prokka HMM download rule

    @fmalmeida
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  7. added label to use docker for tools

    @fmalmeida
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  8. fixed argminer download

    @fmalmeida
    fmalmeida committed Nov 19, 2021
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  9. fixed victors download

    @fmalmeida
    fmalmeida committed Nov 19, 2021
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  10. fixed iceberg download

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  11. prokka using given database and bioconda image

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  12. docker specific for downloading databases

    @fmalmeida
    fmalmeida committed Nov 19, 2021
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  13. update packages

    @fmalmeida
    fmalmeida committed Nov 19, 2021
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  14. added mlst database download rule

    @fmalmeida
    fmalmeida committed Nov 19, 2021
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  15. add bacannot db info

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    fmalmeida committed Nov 19, 2021
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  16. also downloads PGAP db

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Commits on Nov 20, 2021

  1. added prokka and mlst

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  2. fix conditional

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  3. fixed pgap conditional

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  4. added barrnap

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Commits on Nov 21, 2021

  1. added 'compute_gc' module -- think about modules with two tools

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Commits on Dec 6, 2021

  1. adding identation

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  2. fixing label

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    fmalmeida committed Dec 6, 2021
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  3. first tries on conda envs

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  4. removing label

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  5. adding plasmidfinder

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    fmalmeida committed Dec 6, 2021
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  6. added platon

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Commits on Dec 15, 2021

  1. working until islandpath

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  2. added: VFDB

    @fmalmeida
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  3. added: Victors

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  4. changing name and organization of MISC image

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  5. added: PHAST

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Commits on Dec 16, 2021

  1. added: phigaro

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Commits on Dec 17, 2021

  1. added: phispy

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  2. added: iceberg

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    fmalmeida committed Dec 17, 2021
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  3. added: kofamscan db download

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    fmalmeida committed Dec 17, 2021
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Commits on Dec 21, 2021

  1. removing named outputs as it will be solved in another PR

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  2. added: kofamscan from downloaded database

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  3. added: kegg_decoder

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Commits on Jan 6, 2022

  1. Refactor channel identifiers and process names (#45) 

    **Main change**

Processes, channels and workflow names have had its case names changed in order to meet nextflow's community standards.

**Commits**
* Refactor names
* refactor names in the workflows
* Update workflows/bacannot.nf
* Update workflows/bacannot.nf
* Apply suggestions from code review
* Update workflows/bacannot.nf wrt iceberg
* Accomodate code review and fix the channel name
* fix MERGE_ANNOTATIONS process case in line 331

Co-authored-by: Felipe Marques de Almeida <[email protected]>
    @abhi18av @fmalmeida
    abhi18av and fmalmeida authored Jan 6, 2022
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  2. Merge branch 'develop' into remodeling

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Commits on Jan 12, 2022

  1. trying to brind amrfinder, card_rgi and argminer

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  2. trying to fix how the scale is calculated for amrfinder

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  3. changing scale to perl

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    fmalmeida committed Jan 12, 2022
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  4. typo fix

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    fmalmeida committed Jan 12, 2022
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  5. removing unnecessary comma

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Commits on Jan 13, 2022

  1. Update amrfinder.nf 

    passing calculation of thresold into two decimals scale to groovy
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  2. properly working until amrfinder and card_rgi

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Commits on Jan 20, 2022

  1. added small dataset test profile

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  2. Merge branch 'develop' into remodeling

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  3. fixing name of quicktest profile

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Commits on Jan 21, 2022

  1. fixing urls of testing samplesheets

    @fmalmeida
    fmalmeida committed Jan 21, 2022
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  2. removing unnecessary files

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    fmalmeida committed Jan 21, 2022
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  3. Merge branch 'develop' into remodeling

    @fmalmeida
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Commits on Jan 25, 2022

  1. Merge branch 'master' into remodeling

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Commits on Jan 26, 2022

  1. fix missing label

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    fmalmeida committed Jan 26, 2022
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  2. adding resfinder to miscellaneous image

    @fmalmeida
    fmalmeida committed Jan 26, 2022
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  3. fixing gitignore

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    fmalmeida committed Jan 26, 2022
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  4. change manifest to upcoming version

    @fmalmeida
    fmalmeida committed Jan 26, 2022
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  5. updating db download workflow behaviour

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    fmalmeida committed Jan 26, 2022
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  6. removing .git dirs

    @fmalmeida
    fmalmeida committed Jan 26, 2022
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  7. fixing argminder download

    @fmalmeida
    fmalmeida committed Jan 26, 2022
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  8. properly added resfinder

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Commits on Jan 31, 2022

  1. adding script that parses nanopolish methyl call

    @fmalmeida
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  2. removing unnecessary labels

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    fmalmeida committed Jan 31, 2022
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Commits on Feb 9, 2022

  1. starting to change how images are done

    @fmalmeida
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  2. added perl tools 

    Added:

* prokka
* barrnap
* mlst
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  3. added misc module 

    added:

* gc_compute module
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  4. adding labels

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  5. added kofam analysis

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    fmalmeida committed Feb 9, 2022
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  6. added main pyenv 

    added tools:

* platon
* plasmidfinder
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  7. fixed perlenv image 

    Added tool:

* islandpath
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  8. included virulence modules 

    they use the miscellaneous image
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  9. pyenv image updated 

    added prophage tools:

* phast scan
* phigaro
*phispy
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  10. added iceberg db module 

    it uses the miscellaneous image
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Commits on Feb 10, 2022

  1. added py36env image 

    added tool:

* rgi
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  2. added resistance tools 

    added:

* argminer db module
* resfinder
* amrfinderplus
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  3. added nanopolish

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  4. added refseq_masher

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Commits on Feb 15, 2022

  1. added digIS 

    Docker image and modules were updated to run until digIS
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Commits on Feb 16, 2022

  1. added antismash

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  2. added sequence server

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Commits on Feb 17, 2022

  1. added merge_annotation module

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  2. added draw_gis modules

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  3. added gff2gbk module

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  4. added create_sql module

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  5. added first resource management labels

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  6. fixing resouce label for phigaro

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  7. little finx in env

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Commits on Feb 18, 2022

  1. fixing how tuples should be passed

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  2. arrived at jbrowse step

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  3. fixing draw_gis module input tuple

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  4. jbrowse added

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Commits on Feb 20, 2022

  1. Create test_pr.yml 

    This is how new versions will be organised after the remodeling branch update, and, therefore, the test_pr must be updated.
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  2. Merge branch 'master' into remodeling

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  3. fixed phast db incorporation

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  4. fixing inputs on report

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  5. Update test_pr.yml 

    Will only act in ready for review PRs
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  6. Merge branch 'master' into remodeling

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  7. adding ENV VAR for current version

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  8. adding scripts to automatically build images

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  9. fixed iceberg db incorporation

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Commits on Feb 22, 2022

  1. Update digIS.nf 

    DIGis gff usage fixed
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Commits on Feb 23, 2022

  1. fixed vfdb incorporation

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  2. changing file to path input resolution

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  3. fixed victors db incorporation

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  4. changed channel names in main script

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  5. fixed argminer and prokka tables

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  6. fixed custom db annotations incorporation

    @fmalmeida
    fmalmeida committed Feb 23, 2022
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Commits on Mar 1, 2022

  1. fixed bacannot server loading

    @fmalmeida
    fmalmeida committed Mar 1, 2022
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  2. fixed custom db reports

    @fmalmeida
    fmalmeida committed Mar 1, 2022
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  3. begin incorporation of nf-core framework

    @fmalmeida
    fmalmeida committed Mar 1, 2022
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Commits on Mar 2, 2022

  1. nf-core libs have been added to the pipeline

    @fmalmeida
    fmalmeida committed Mar 2, 2022
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  2. custom database annotation added to JBrowse

    @fmalmeida
    fmalmeida committed Mar 2, 2022
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  3. fixed custom database gff generation

    @fmalmeida
    fmalmeida committed Mar 2, 2022
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  4. Update Dockerfile 

    diminished image size by removing antismash db from inside it
    @fmalmeida
    fmalmeida committed Mar 2, 2022
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  5. Update docker.config 

    uncommenting assemblers images
    @fmalmeida
    fmalmeida committed Mar 2, 2022
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  6. creating singularity profile

    @fmalmeida
    fmalmeida committed Mar 2, 2022
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  7. begin documentation update

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    fmalmeida committed Mar 2, 2022
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Commits on Mar 3, 2022

  1. added singularity profile

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    fmalmeida committed Mar 3, 2022
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  2. made image compatible with earlier versions

    @fmalmeida
    fmalmeida committed Mar 3, 2022
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  3. given 777 permissions to workdir

    @fmalmeida
    fmalmeida committed Mar 3, 2022
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  4. adjusted default values

    @fmalmeida
    fmalmeida committed Mar 3, 2022
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  5. fixed prokka to work with singularity

    @fmalmeida
    fmalmeida committed Mar 3, 2022
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Commits on Mar 4, 2022

  1. fixed rgi for singularity usage

    @fmalmeida
    fmalmeida committed Mar 4, 2022
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Commits on Mar 9, 2022

  1. updating PR test action

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    fmalmeida committed Mar 9, 2022
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  2. update targeted branches

    @fmalmeida
    fmalmeida committed Mar 9, 2022
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  3. limiting process resources

    @fmalmeida
    fmalmeida committed Mar 9, 2022
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  4. updated image for singularity

    @fmalmeida
    fmalmeida committed Mar 9, 2022
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  5. removing unused dbs in quicktest

    @fmalmeida
    fmalmeida committed Mar 9, 2022
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  6. not using big dbs in quicktest

    @fmalmeida
    fmalmeida committed Mar 9, 2022
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  7. Update resfinder.nf

    @fmalmeida
    fmalmeida committed Mar 9, 2022
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Commits on Mar 17, 2022

  1. adding gitpod config

    @fmalmeida
    fmalmeida committed Mar 17, 2022
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  2. fixed yml

    @fmalmeida
    fmalmeida committed Mar 17, 2022
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  3. fixing custom db report getattributefileld snippet

    @fmalmeida
    fmalmeida committed Mar 17, 2022
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  4. begin change to mkdocs

    @fmalmeida
    fmalmeida committed Mar 17, 2022
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  5. add requirements

    @fmalmeida
    fmalmeida committed Mar 17, 2022
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  6. Update .readthedocs.yml

    @fmalmeida
    fmalmeida committed Mar 17, 2022
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  7. Update .readthedocs.yml

    @fmalmeida
    fmalmeida committed Mar 17, 2022
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  8. Update .readthedocs.yml

    @fmalmeida
    fmalmeida committed Mar 17, 2022
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  9. Update .readthedocs.yml

    @fmalmeida
    fmalmeida committed Mar 17, 2022
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  10. update

    @fmalmeida
    fmalmeida committed Mar 17, 2022
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Commits on Mar 21, 2022

  1. update requirements

    @fmalmeida
    fmalmeida committed Mar 21, 2022
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  2. added index

    @fmalmeida
    fmalmeida committed Mar 21, 2022
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  3. fixed tags

    @fmalmeida
    fmalmeida committed Mar 21, 2022
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  4. added installation information

    @fmalmeida
    fmalmeida committed Mar 21, 2022
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  5. now on quickstart

    @fmalmeida
    fmalmeida committed Mar 21, 2022
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  6. changed some admonitions

    @fmalmeida
    fmalmeida committed Mar 21, 2022
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  7. added quickstart

    @fmalmeida
    fmalmeida committed Mar 21, 2022
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Commits on Mar 22, 2022

  1. added samplesheet page to mkdocs

    @fmalmeida
    fmalmeida committed Mar 22, 2022
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  2. included dir with images

    @fmalmeida
    fmalmeida committed Mar 22, 2022
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  3. Update samplesheet.md 

    fixed header levels
    @fmalmeida
    fmalmeida committed Mar 22, 2022
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  4. outputs page added to mkdocs

    @fmalmeida
    fmalmeida committed Mar 22, 2022
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  5. Update standard.config 

    removing "paralallel_jobs" definition
    @fmalmeida
    fmalmeida committed Mar 22, 2022
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  6. Update defaults.config 

    fixed blast default values
    @fmalmeida
    fmalmeida committed Mar 22, 2022
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  7. updated and tested quickstart

    @fmalmeida
    fmalmeida committed Mar 22, 2022
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  8. updating gitpod.yml

    @fmalmeida
    fmalmeida committed Mar 22, 2022
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  9. creates a testing dir with more space

    @fmalmeida
    fmalmeida committed Mar 22, 2022
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Commits on Mar 23, 2022

  1. added profile selection information

    @fmalmeida
    fmalmeida committed Mar 23, 2022
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  2. Merge branch 'remodeling' of https://github.com/fmalmeida/bacannot in… 

    …to remodeling
    @fmalmeida
    fmalmeida committed Mar 23, 2022
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  3. Update manual.md 

    manual updated for mkdocs and with new --ncbi_proteins parameter
    @fmalmeida
    fmalmeida committed Mar 23, 2022
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  4. Update nextflow_schema.json 

    updated --custom_db parameter description
    @fmalmeida
    fmalmeida committed Mar 23, 2022
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  5. Update nextflow.config 

    removed parameters that are in default and should not be in the boilerplate
    @fmalmeida
    fmalmeida committed Mar 23, 2022
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  6. added config file page

    @fmalmeida
    fmalmeida committed Mar 23, 2022
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  7. information about custom databases added

    @fmalmeida
    fmalmeida committed Mar 23, 2022
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Commits on Mar 24, 2022

  1. Update nextflow_schema.json

    @fmalmeida
    fmalmeida committed Mar 24, 2022
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  2. defaults need to be loaded before boilerplate

    @fmalmeida
    fmalmeida committed Mar 24, 2022
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  3. changing label of unicycler and flye

    @fmalmeida
    fmalmeida committed Mar 24, 2022
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Commits on Mar 26, 2022

  1. fixed antismash installation

    @fmalmeida
    fmalmeida committed Mar 26, 2022
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  2. fixed keggdecoder requires py36

    @fmalmeida
    fmalmeida committed Mar 26, 2022
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  3. fixed resfinder module 

    fixed db setup
    @fmalmeida
    fmalmeida committed Mar 26, 2022
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  4. pipeline fixed for docker

    @fmalmeida
    fmalmeida committed Mar 26, 2022
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